layout	permalink	title	header1	header2	image	keywords	description	instructors	length
workshop_main_3day	/HTG_2021	HTseq	Workshop Pages for Students	High Throughput Genomics Analysis	/site_images/CBW_High-throughput_icon.jpg	Map sequence data, De Novo assembly tasks, Quantify sequence data	Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data, where the focus is on Illumina reads although information is applicable to all sequencer reads.	Jared Simpson, Mathieu Bourgey	3 days

Welcome

The course schedule can be found here

Meet your faculty here

Pre-Workshop Materials

Pre-work including programs to install can be found here

AWS Module

Connecting and properly using a cloud computing cluster at the CBW here

Class Photo

Comming soon

Day 1

Welcome

Rachade Hmamouchi

Module 1: Introduction

Jared Simpson

Lecture: Introduction to Sequencing Technologies

Lecture: Introduction to HTS file formats

Module 2: data vizualization with IGV

Rob Syme

Module 3: Genome Alignment

Mathieu Bourgey

Day 2

Module 3: Genome Alignment

Mathieu Bourgey

Module 4: Single nucleotide variant Calling

Mathieu Bourgey

Day 3

Module 5: Structural Variant Calling

Rob Syme

Module 6: Genome Assembly

Jared Simpson

Survey